* [PATCH] gnu: Add crossmap.
@ 2015-02-26 15:38 Ricardo Wurmus
2015-02-28 14:53 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-02-26 15:38 UTC (permalink / raw
To: Guix-devel
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From e93da9b48bafbbfa56fe348cabad9e074eda63fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 26 Feb 2015 16:34:49 +0100
Subject: [PATCH] gnu: Add crossmap.
* gnu/packages/bioinformatics.scm (crossmap): New variable.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
---
gnu-system.am | 1 +
gnu/packages/bioinformatics.scm | 42 ++++++++
.../patches/crossmap-allow-system-pysam.patch | 113 +++++++++++++++++++++
3 files changed, 156 insertions(+)
create mode 100644 gnu/packages/patches/crossmap-allow-system-pysam.patch
diff --git a/gnu-system.am b/gnu-system.am
index e42e89a..a500ec7 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -375,6 +375,7 @@ dist_patch_DATA = \
gnu/packages/patches/cpio-CVE-2014-9112-pt5.patch \
gnu/packages/patches/cpio-gets-undeclared.patch \
gnu/packages/patches/cpufrequtils-fix-aclocal.patch \
+ gnu/packages/patches/crossmap-allow-system-pysam.patch \
gnu/packages/patches/cssc-gets-undeclared.patch \
gnu/packages/patches/cssc-missing-include.patch \
gnu/packages/patches/clucene-contribs-lib.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1103d92..749d0a0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -272,6 +272,48 @@ gapped, local, and paired-end alignment modes.")
"CLIPper is a tool to define peaks in CLIP-seq datasets.")
(license license:gpl2)))
+(define-public crossmap
+ (package
+ (name "crossmap")
+ (version "0.1.6")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp"))
+ ;; patch has been sent upstream already
+ (patches (list
+ (search-patch "crossmap-allow-system-pysam.patch")))
+ (modules '((guix build utils)))
+ ;; remove bundled copy of pysam
+ (snippet
+ '(delete-file-recursively "lib/pysam"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (alist-cons-after
+ 'unpack 'set-env
+ (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
+ %standard-phases)))
+ (inputs
+ `(("python-numpy" ,python2-numpy)
+ ("python-pysam" ,python2-pysam)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("python-cython" ,python2-cython)
+ ("python-nose" ,python2-nose)
+ ("python-setuptools" ,python2-setuptools)))
+ (home-page "http://crossmap.sourceforge.net/")
+ (synopsis "Convert genome coordinates between assemblies")
+ (description
+ "CrossMap is a program for conversion of genome coordinates or annotation
+files between different genome assemblies. It supports most commonly used
+file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
+ (license license:gpl2+)))
+
(define-public flexbar
(package
(name "flexbar")
diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch
new file mode 100644
index 0000000..a16f901
--- /dev/null
+++ b/gnu/packages/patches/crossmap-allow-system-pysam.patch
@@ -0,0 +1,113 @@
+diff --git a/setup.py b/setup.py
+--- a/setup.py 2015-02-26 15:28:49.771189185 +0100
++++ b/setup.py 2015-02-26 15:55:03.440327752 +0100
+@@ -19,6 +19,15 @@
+ except:
+ have_numpy = False
+
++try:
++ import pysam
++ if os.environ['CROSSMAP_USE_SYSTEM_PYSAM']:
++ have_pysam = True
++ else:
++ have_pysam = False
++except ImportError:
++ have_pysam = False
++
+ if platform.system()=='Windows':
+ print >> sys.stderr, "Sorry, Windows platform is not supported!"
+ sys.exit()
+@@ -165,49 +174,50 @@
+
+
+ #================= pysam samtools ====================
+- extensions.append(Extension(
+- "pysam.csamtools",
+- csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
+- glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
+- os_c_files + \
+- glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
+- library_dirs=[],
+- include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
+- libraries=[ "z", ],
+- language="c",
+- define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')],
+- ))
+-
+- extensions.append(Extension(
+- "pysam.ctabix",
+- tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
+- os_c_files + \
+- glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
+- library_dirs=[],
+- include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
+- libraries=[ "z", ],
+- language="c",
+- define_macros = [('_FILE_OFFSET_BITS','64'),
+- ('_USE_KNETFILE','')],
+- ))
+-
+- extensions.append(Extension(
+- "pysam.TabProxies",
+- tabproxies_sources + os_c_files,
+- library_dirs=[],
+- include_dirs= include_os,
+- libraries=[ "z", ],
+- language="c",
+- ))
+-
+- extensions.append(Extension(
+- "pysam.cvcf",
+- cvcf_sources + os_c_files,
+- library_dirs=[],
+- include_dirs= ["lib/tabix",] + include_os,
+- libraries=[ "z", ],
+- language="c",
+- ))
++ if not have_pysam:
++ extensions.append(Extension(
++ "pysam.csamtools",
++ csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
++ glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
++ os_c_files + \
++ glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
++ library_dirs=[],
++ include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
++ libraries=[ "z", ],
++ language="c",
++ define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')],
++ ))
++
++ extensions.append(Extension(
++ "pysam.ctabix",
++ tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
++ os_c_files + \
++ glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
++ library_dirs=[],
++ include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
++ libraries=[ "z", ],
++ language="c",
++ define_macros = [('_FILE_OFFSET_BITS','64'),
++ ('_USE_KNETFILE','')],
++ ))
++
++ extensions.append(Extension(
++ "pysam.TabProxies",
++ tabproxies_sources + os_c_files,
++ library_dirs=[],
++ include_dirs= include_os,
++ libraries=[ "z", ],
++ language="c",
++ ))
++
++ extensions.append(Extension(
++ "pysam.cvcf",
++ cvcf_sources + os_c_files,
++ library_dirs=[],
++ include_dirs= ["lib/tabix",] + include_os,
++ libraries=[ "z", ],
++ language="c",
++ ))
+
+
+ return extensions
--
2.1.0
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] gnu: Add crossmap.
2015-02-26 15:38 [PATCH] gnu: Add crossmap Ricardo Wurmus
@ 2015-02-28 14:53 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-02-28 14:53 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: Guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From e93da9b48bafbbfa56fe348cabad9e074eda63fb Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 26 Feb 2015 16:34:49 +0100
> Subject: [PATCH] gnu: Add crossmap.
>
> * gnu/packages/bioinformatics.scm (crossmap): New variable.
> * gnu/packages/patches/crossmap-allow-system-pysam.patch: New file.
> * gnu-system.am (dist_patch_DATA): Add it.
[...]
> diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch
> new file mode 100644
> index 0000000..a16f901
> --- /dev/null
> +++ b/gnu/packages/patches/crossmap-allow-system-pysam.patch
Please add a comment at the top of this file explaining what it does and
what its upstream status is.
OK to commit with this change.
Thanks,
Ludo’.
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2015-02-28 14:53 ` Ludovic Courtès
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